2-genetics project

This is my R project for genetics The graph results are in the folder ./deliverables/

Steps and results

  1. extract GSM matrix (.mtx) files as counts
  • reduced samples to just correspond to LCMV_GP66+ (“GSM3543444” & “GSM3543448”) and TILs_CD44+_PD+ (“GSM3543446” “GSM3543449”)
  • deleted any gene with below 1 CPM across all columns
  • TMM normalized gene epression and converted to Log-CPM
  • Used the treat method to find genes with significant cell type difference of LogFC greater than 2
    • This left 12 genes with signficant difference across group
  • Used Independent 2 group Whitney-Man U test (a=.05) to test for differences between batches across each of the selected samples
    • within groups, batches were all but twice (out of 12) significantly different from each other, suggesting significant batch differences.
  • Analyze reproducibility

Plots and Results: pic pic pic pic pic pic pic pic pic pic pic pic

To-do:

[x] add /GSE124691/ to gitignore [x] add 2-genetics/scratch/** to gitignore